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    <title>Identification - NIST MS Search</title>
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<h1>Identification - NIST MS Search</h1>

<h2>Description</h2>

<p>
    This module allows the identification of chromatographic peaks using the <a
        href="http://chemdata.nist.gov/mass-spc/ms-search/">NIST MS Search</a> program.
</p>

<p>
    NIST MS Search accepts spectra as input to its searches. Each spectrum is defined by a list of (mass, intensity)
    pairs. The module forms a query spectrum for each row in the peak list. For each peak-list row <span
        style="font-style: italic;">P</span> it finds all other peak-list rows whose (average) RTs are within a
    specified tolerance (see <span style="font-style: italic;">Spectrum RT tolerance</span>) of <span
        style="font-style: italic;">P</span>'s RT. The peaks' (neutral) mass and intensity value pairs are combined to
    form a search spectrum for <span style="font-style: italic;">P</span>.
</p>

<p>
    The number of peaks used to form a mass spectrum can be limited by setting the <span style="font-style: italic;">Max.
    peaks per spectrum</span> parameter to a value greater than zero. If this parameter is set to <span
        style="font-style: italic;">N</span> then the <span style="font-style: italic;">N</span> rows whose RTs are
    closest to that of the row (and within the specified RT tolerance) are used to form the mass spectrum.
</p>

<p>
    The module can also be run for an individual row of the peak-list table by highlighting the row and then selecting
    <span style="font-style: italic;">NIST MS Search</span> from the pop-up menu (right mouse-button click). In such
    cases, the mass spectrum passed to NIST MS Search is formed in the same way as described above.
</p>

<h4>Method Parameters</h4>

<dl>
    <dt>NIST MS Search directory</dt>
    <dd>Full path of the directory containing the NIST MS Search executable (nistms$.exe).</dd>

    <dt>Ionization method</dt>
    <dd>Type of ionization that produced the peak subjected to identification. This is used to calculate the neutral
        mass.
    </dd>

    <dt>Spectrum RT tolerance</dt>
    <dd>When forming a search spectrum for a given peak-list row, include all other rows whose (average) RT is within
        the specified tolerance of the given row.
    </dd>

    <dt>Max. peaks per spectrum</dt>
    <dd>When forming a search spectrum for a given peak-list row, include at most the specified number of peaks
        (including the current row). If a row has more than this maximum number of peaks, <span
                style="font-style: italic;">N</span>, whose RTs are within the specified RT tolerance then it is the
        <span style="font-style: italic;">N</span> rows whose RTs are closest to that of the row that are used to form
        the mass spectrum. Setting this parameter to 0 will cause it to be ignored, i.e. all peak-list rows within the
        specified RT tolerance are used to form the mass spectrum.
    </dd>

    <dt>Must have same identities</dt>
    <dd>Two peaks will only be included in the same spectrum if they have the same identity (for use with <a
            href="../../camera/help/help.html">CAMERA pseudo-spectra</a>)
    </dd>

    <dt>Min. match factor</dt>
    <dd>NIST MS Search calculates a match factor (0 .. 999) between the submitted spectrum and each hit. Ignore hits
        with a match factor below the given threshold.
    </dd>

    <dt>Min. reverse match factor</dt>
    <dd>NIST MS Search calculates a <span style="font-style: italic;">reverse</span> match factor (0 .. 999) between the
        submitted spectrum and each hit. Ignore hits with a reverse match factor below the given threshold.
    </dd>
</dl>

<h3>Requirements</h3>

<p>
    This module relies on the NIST MS Search software, which is currently only available for Microsoft Windows, being
    installed.
</p>

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